/*
 * Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University, Bilkent University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without modification,
 * are permitted provided that the following conditions are met:
 *
 * Redistributions of source code must retain the above copyright notice, this list
 * of conditions and the following disclaimer.
 * - Redistributions in binary form must reproduce the above copyright notice, this
 *   list of conditions and the following disclaimer in the documentation and/or other
 *   materials provided with the distribution.
 * - Neither the names of the University of Washington, Simon Fraser University, 
 *   nor the names of its contributors may be
 *   used to endorse or promote products derived from this software without specific
 *   prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

/*
  Authors: 
  Farhad Hormozdiari
  Faraz Hach
  Can Alkan
  Emails: 
  farhadh AT uw DOT edu
  fhach AT cs DOT sfu DOT ca
  calkan AT cs DOT bilkent DOT edu DOT tr
*/


#include <stdio.h>
#include <stdlib.h>
#include <zlib.h>
#include <string.h>
#include "Common.h"
#include "Output.h"

FILE			*_out_fp;
gzFile			_out_gzfp;

char buffer[300000];
int bufferSize = 0;


void finalizeGZOutput()
{
  gzclose(_out_gzfp);
}

void finalizeTXOutput()
{
  fclose(_out_fp);
}


void gzOutputQ(SAM map)
{
  gzprintf(_out_gzfp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s", 
	   map.QNAME, 
	   map.FLAG,
	   map.RNAME, 
	   map.POS,
	   map.MAPQ,
	   map.CIGAR,
	   map.MRNAME,
	   map.MPOS,
	   map.ISIZE,
	   map.SEQ,
	   map.QUAL);
	
  int i;

  for ( i = 0; i < map.optSize; i++)
    {
      switch (map.optFields[i].type)
	{
	case 'A':
	  gzprintf(_out_gzfp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
	  break;
	case 'i':
	  gzprintf(_out_gzfp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
	  break;
	case 'f':
	  gzprintf(_out_gzfp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
	  break;
	case 'Z':
	case 'H':
	  gzprintf(_out_gzfp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
	  break;
	}
    }

  if (readGroup[0] != 0)
    gzprintf(_out_gzfp, "\t%s:%c:%s", "RG", 'Z', readGroup);

  gzprintf(_out_gzfp, "\n");
}

void outputSAM(FILE *fp, SAM map)
{
  fprintf(fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s",
	  map.QNAME,
	  map.FLAG,
	  map.RNAME,
	  map.POS,
	  map.MAPQ,
	  map.CIGAR,
	  map.MRNAME,
	  map.MPOS,
	  map.ISIZE,
	  map.SEQ,
	  map.QUAL);


  int i;

  for ( i = 0; i < map.optSize; i++)
    {
      switch (map.optFields[i].type)
	{
	case 'A':
	  fprintf(fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
	  break;
	case 'i':
	  fprintf(fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
	  break;
	case 'f':
	  fprintf(fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
	  break;
	case 'Z':
	case 'H':
	  fprintf(fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
	  break;
	}
    }

  if (readGroup[0] != 0)
    fprintf(fp, "\t%s:%c:%s", "RG", 'Z', readGroup);

  fprintf(fp, "\n");

}

void outputQ(SAM map)
{

  fprintf(_out_fp, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s", 
	  map.QNAME, 
	  map.FLAG,
	  map.RNAME, 
	  map.POS,
	  map.MAPQ,
	  map.CIGAR,
	  map.MRNAME,
	  map.MPOS,
	  map.ISIZE,
	  map.SEQ,
	  map.QUAL);

	
  int i;

  for ( i = 0; i < map.optSize; i++)
    {
      switch (map.optFields[i].type)
	{
	case 'A':
	  fprintf(_out_fp, "\t%s:%c:%c", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].cVal);
	  break;
	case 'i':
	  fprintf(_out_fp, "\t%s:%c:%d", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].iVal);
	  break;
	case 'f':
	  fprintf(_out_fp, "\t%s:%c:%f", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].fVal);
	  break;
	case 'Z':
	case 'H':
	  fprintf(_out_fp, "\t%s:%c:%s", map.optFields[i].tag, map.optFields[i].type, map.optFields[i].sVal);
	  break;
	}
    }

  if (readGroup[0] != 0)
    fprintf(_out_fp, "\t%s:%c:%s", "RG", 'Z', readGroup);
	
  fprintf(_out_fp, "\n");
}

int initOutput ( char *fileName, int compressed)
{
  if (compressed)
    {
      char newFileName[strlen(fileName)+4];
      sprintf(newFileName, "%s.gz", fileName);

      _out_gzfp = fileOpenGZ(newFileName, "w1f");
      if (_out_gzfp == Z_NULL)
	{
	  return 0;
	}
      finalizeOutput = &finalizeGZOutput;

      output = &gzOutputQ;
      SAMheaderGZ(_out_gzfp);
    }
  else
    {
      _out_fp = fileOpen(fileName, "w");
      if (_out_fp == NULL)
	{
	  return 0;
	}
      finalizeOutput = &finalizeTXOutput;
      output = &outputQ;
      SAMheaderTX(_out_fp, 1);
    }
  buffer[0] = '\0';
  return 1;
}

FILE* getOutputFILE() 
{
  if(_out_fp != NULL)
    return _out_fp;
  else if(_out_gzfp != NULL)
    return (FILE *)_out_gzfp;
  else
    return NULL;
}
void SAMheaderTX(FILE *outfp, int check)
{
  FILE *fp;
  char fainame[FILE_NAME_LENGTH];
  char chrom[FILE_NAME_LENGTH];
  int chromlen;
  char rest[FILE_NAME_LENGTH];
  char *ret;

  sprintf(fainame, "%s.fai",fileName[0]);
  fp = fopen(fainame, "r");

  if (fp != NULL){
    fprintf(outfp, "@HD\tVN:1.4\tSO:unknown\n");
    
    while (fscanf(fp, "%s\t%d\t", chrom, &chromlen) > 0){
      ret = fgets(rest, FILE_NAME_LENGTH, fp);
      fprintf(outfp, "@SQ\tSN:%s\tLN:%d\n", chrom, chromlen);
    }
    fclose(fp);

    if (readGroup[0] != 0 && sampleName[0] != 0)
      fprintf(outfp, "@RG\tID:%s\tSM:%s\tLB:%s\tPL:illumina\n", readGroup, sampleName, libName);
    
    fprintf(outfp, "@PG\tID:mrFAST\tPN:mrFAST\tVN:%s.%s\n",  versionNumber, versionNumberF);
  }
  else if (check){
    fprintf(stdout, "WARNING: %s.fai not found, the SAM file(s) will not have a header.\n", fileName[0]);
    fprintf(stdout, "You can generate the .fai file using samtools. Please place it in the same directory with the index to enable SAM headers.\n");
  }

  ret++;
}

void SAMheaderGZ(gzFile outgzfp)
{
  FILE *fp;
  char fainame[FILE_NAME_LENGTH];
  char chrom[FILE_NAME_LENGTH];
  int chromlen;
  char rest[FILE_NAME_LENGTH];
  char *ret;

  sprintf(fainame, "%s.fai",fileName[0]);
  fp = fopen(fainame, "r");

  if (fp != NULL){
    gzprintf(outgzfp, "@HD\tVN:1.4\tSO:unknown\n");

    while (fscanf(fp, "%s\t%d\t", chrom, &chromlen) > 0){
      ret = fgets(rest, FILE_NAME_LENGTH, fp); 
      gzprintf(outgzfp, "@SQ\tSN:%s\tLN:%d\n", chrom, chromlen);
    }
    fclose(fp);

    if (readGroup[0] != 0 && sampleName[0] != 0)
      gzprintf(outgzfp, "@RG\tID:%s\tSM:%s\tLB:%s\tPL:illumina\n", readGroup, sampleName, libName);

    gzprintf(outgzfp, "@PG\tID:mrFAST\tPN:mrFAST\tVN:%s.%s\n",  versionNumber, versionNumberF);
  }
  else{
    fprintf(stdout, "WARNING: %s.fai not found, the SAM file(s) will not have a header.\n", fileName[0]);
    fprintf(stdout, "You can generate the .fai file using samtools. Please place it in the same directory with the index to enable SAM headers.\n");
  }

  ret++;
}



